Executable compenium template

[chainsawriot]

Following up this discussion, a usethis style compendium could be considered.

But, there are so many compendium formats available. We need to think about interoperability rather than XKCD 927.

R specific

• https://github.com/ropensci/rrrpkg
• https://github.com/benmarwick/rrtools paper
• https://github.com/FRBCesab/rcompendium/
• https://github.com/Pakillo/template
• https://github.com/jhollist/manuscriptPackage
• https://cran.r-project.org/web/packages/ProjectTemplate/

Sweave

• https://journal.r-project.org/archive/2011/RJ-2011-013/RJ-2011-013.pdf
• https://www.klinikum.uni-heidelberg.de/fileadmin/inst_med_biometrie/pdf/compHuang.pdf

Not R specific but can also be used to run R

• https://github.com/ccs-amsterdam/compendium

(white)papers

• https://docs.google.com/document/d/1LzZKS44y4OEJa4Azg5reGToNAZL0e0HSUwxamNY7E-Y/edit

[chainsawriot]

How about we just use the structure of Turing (rather than inventing something new):

compendium/
├── CITATION
├── code
│   ├── analyse_data.R
│   └── clean_data.R
├── data_clean
│   └── data_clean.csv
├── data_raw
│   ├── datapackage.json
│   └── data_raw.csv
├── Dockerfile
├── figures
│   └── flow_chart.jpeg
├── LICENSE
├── Makefile
├── paper.Rmd
└── README.md

It means that:

• We copy the materials_dir (assume that it contains data_*, code and paper.Rmd) as the output_dir.
• Place Dockerfile
• Create a directory called rang (or even ./inst/rang) and put cache (if cache is TRUE) and rang.R there.
• In the Dockerfile, just COPY * /*
• Rewire the current Dockerfile to RUN rang/rang.R
• Rewire cache to rang/cache in rang/rang.R

[schochastics]

I was comparing the compendiums the other day and I also like the Turing way best. Lets go with that one.

[chainsawriot]

Maybe inst/rang is a better idea because we can also cover rrtools. We can just have a function called rang::use_rang() to insert our rang things into a format-independent existing compendium directory. We can also provide a function called rang::use_turing() to generate a basic structure.

Potential features / issues

• [ ] Makefile detection to insert make as a sysreqs
• [ ] How about rrtools' Quarto?
• [ ] Is this real?

[schochastics]

I like the use_* approach. eventually one could also implement other compendiums like this. Can you help me understand the "is this real" comment. Is that a GHA to build a docker image?

[chainsawriot]

Quote from the readme

this also creates creates a minimal .yml configuration file to activate continuous integration using GitHub Actions. This will attempt to render your qmd document, in a Docker container specified by your Dockerfile, each time you push to GitHub.

With this default Dockerfile

https://github.com/benmarwick/rrtools/blob/f71bddccf00d124512a8f20a4df08cd5e069f53e/inst/templates/Dockerfile#L1-L22

Too good to be true, e.g. no installation of Quarto CLI. But well, it says "attempt".

[schochastics]

oh ok that would be something :-O

[chainsawriot]

Tasks

• [x] use_rang
• [x] use_turing create_turing
• [x] A vignette
• [x] Integration of apptainer
• [x] Don't use ... in create_turing

[chainsawriot]

https://github.com/gesistsa/rang/issues/159#issuecomment-1751719183